Skill Claude CodeCodex
Build enhancer-driven gene regulatory networks (eRegulons) from paired scRNA+scATAC multiome data using SCENIC+, with a FigR alternative in R.
111 1mo ago A 44 tokens
Skill Claude CodeCodex
Normalize raw RNA-seq count matrices: pre-filter genes, estimate between-sample size factors (RLE/TMM), compute TPM, variance-stabilize for visualization, correct GC/length bias, and normalize single-cell data.
111 1mo ago A 51 tokens
Skill Claude CodeCodex
Annotate ChIP-seq / ATAC-seq peaks with gene features, ENCODE cCRE regulatory classes, and gene-set enrichment using ChIPseeker, HOMER, rGREAT, and ChIP-Enrich.
111 1mo ago A 53 tokens
Skill Claude CodeCodex
Analyze a single-cell pooled CRISPR perturbation screen: assign sgRNAs to cells, filter escapers via Mixscape, fit per-gene differential expression (SCEPTRE/PyDESeq2), and rank perturbations by molecular effect.
111 1mo ago A 58 tokens
Skill Claude CodeCodex
Analyze Perturb-seq CRISPR screens by linking guide RNA assignments to single-cell transcriptional phenotypes using pertpy and Seurat Mixscape.
111 1mo ago A 38 tokens
Skill Claude CodeCodex
Assign cell types to segmented IMC single cells from protein marker expression via Leiden clustering, manual gating, or SOM/supervised classification.
111 1mo ago A 33 tokens
Skill Claude CodeCodex
Preprocess scRNA-seq data: QC metrics, filtering, normalization, highly variable gene selection, and scaling for downstream analysis. Covers Scanpy (Python) and Seurat (R).
111 1mo ago A 43 tokens
Skill Claude CodeCodex
Analyze single-cell ATAC-seq data: QC, LSI dimensionality reduction, clustering, peak calling, and motif activity scoring.
111 1mo ago A 34 tokens
Skill Claude CodeCodex
Infer transcription factor regulons from scRNA-seq with the pySCENIC three-step pipeline (GRNBoost2 → cisTarget → AUCell) plus downstream interpretation.
111 1mo ago A 44 tokens
Skill Claude CodeCodex
Analyze single-cell TCR/BCR immune receptor data with scRNA-seq gene expression using scirpy for joint clonotype and cell-state analysis.
111 1mo ago A 37 tokens
Skill Claude CodeCodex
Complete single-cell RNA-seq workflow from 10X Cell Ranger counts to annotated cell types, with parallel Seurat (R) and scanpy (Python) paths.
111 1mo ago A 43 tokens
Skill Claude CodeCodex
Process 10X scATAC / Multiome data from cellranger output to clustered, annotated cells with per-cluster peaks; choose Signac / ArchR / SnapATAC2 by language and scale.
111 1mo ago A 50 tokens